Transcript CTRF Leadership Meeting
CTRF Leadership Meeting
June 3, 2002 Institutional Partners
V C U G M U
I N O V A
Minutes
5/06/02
Corrections Approval
Principle Objective
Develop Infrastructure and Intellectual Property that Enhances the Competitiveness of the Partners for Clinical and Extramural Funds
Research Objective
Evaluate gene expression (and genetic changes) in human brain, ovarian, breast and hematopoetic cancers
Link gene expression (and genetic changes) to clinical findings and clinical laboratory findings (including histopathological diagnoses) in a common database
Evaluate linked data using bioinformatics
Funding From CTRF
Chandhoke Grant Christensen Fryxell Jamison
Year 1 $325,000
Total (3 yrs)
$975,000 Year 2 $325,000
Torr (Central Admin) Ginder Garrett Buck Guiseppe-Elie Abraham
Year 1 $582,000
Total (3 yrs)
$1,734,603 Year 2 $578,191
Cooper
Year 1 $93,000
Total (3 yrs)
$290,397 Year 2 $96,809
DRAFT
Fiscal Year 2002 Budget Summary Report
CTRF Account # PI
535282 Main Account 535283 Garrett 535284 Buck 535286 Guiseppe-Eli 535285 Ginder 535288 GMU 535286 Inova
June 30 Expenses
$ 33,195.44
$ 9,312.75
Estimated July 1 Balance
$ 43,839.00
$ 169,597.00
Matching Funds to Date
$ 107,728.73
$ 93,382.76
$ 13.24
$ 148,679.03
Reminder - Cost Share Form (VCU)
Cost Share Expenses
Cost share expenditures not paid from cost share linked ledger 4 account must be documented using ‘In Kind/3rd Party Cost Share form’ obtained from Margie Booker’s office . ( http://www.vcu.edu/finance/In kind%20Cost%20Sharing%Certification.pdf
)
FY 02 Rollover
• Rollover process will utilize appropriation adjustments required to be available on July 1, 2002 (Federal fund carry-forward process) • Automated Transaction System (FATS) request must be submitted between June 12 and 14 th – Summary of budget status (Carry-Forward Form) – Justification (Transaction brief) • Justification and Carry-Forward Form to be submitted to Dr. Garrett by June 7, 2002
Request to Carry Forward Form
Justification (Transaction Brief)
Reason for year-end balance:
The project began late. Funds were not identified until 3 months after the programmatic start date. In addition there was a delay in recruitment of key personnel (ex the director of the tissue acquisition service at VCU did not arrive on site until Dec 2002).
Need for carry-forward of these funds:
Use of the unexpended funds are essential to continue the project and carry out the programmatic aims of the grant. There are no alternative funds to achieve the specific aims of the grant. In addition, the institutional partners have already made significant matching obligations to this project.
How the funds will be used:
Funds will be used consistent with the grant proposal
FY 03 Allocation
• [Submit record of expenditures and matching funds (FY02 Closeout)] • Will need to submit progress indicating milestones achieved in FY02 (in prep - C. Garrett)
Website Update
CTRF “News and Updates” page will be added to site
Focus Group roles and responsibility still needed from Focus Group Leaders URL for site is: www.ctrf cagenomics.vcu.edu
SPIN Research
Jo Ann Breaux receiving daily notices of grant opportunities Compiling weekly document of relevant findings Will be distributed over the CTRF LISTSERV
SMART documents currently on the CTRF website
• Training is available: http://www.InfoEd.org/default.stm
Focus Group
Tissue Bank Clinical and Pathology Laboratory Data Database Design Data Analysis Quality Assurance in Microarray Analysis (Chip Fabrication proposed )
Tissue Bank
Focus Group Leaders
Focus Group Leaders
GMU VCU Inova
ClinPath DB Design DataAnalysis QA/LQC Geraldine Grant (GMU) Suhail Nasim (VCU) Barrie Cook (Inova) Lynne Penberthy (VCU) Suhail Nasim (VCU) James Cooper (Inova) James Burgess (Inova) Barrie Cook (Inova) Curtis Jamison (GMU) Lynne Penberthy (VCU) Greg Miller (VCU) Mike Sheriden (Inova) Vikas Chandhoke (GMU) Greg Buck (VCU) Alan Christensen (GMU) Andrea Ferreira-Gonzalez (VCU)
INOVA -CTRF - Tissue Bank
• IRB approval at INOVA • Tissue Acquisition person to be hired and managed by Marianne Smith – Inova to work out process for obtaining necessary informed consent • Tissue Bank person to go to OR area with pathologist responding to request for frozen section and take tissue at that time • Ideal procedure is unclear at this time for tissue acquisition unclear: – Cut and freeze a piece of tissue at the OR (most rapid) – Perform a frozen section on a block and then drop the latter into liquid nitrogen (delay 5-10min) • Protocol handling for Bone Marrow Aspirates not yet specified • Tissue is not to leave Inova until surg path written report is completed
VCU - Tissue Bank
• TAS approved by IRB 4/15/02 • Tissue Bank Staff Activities (Cynthia
Losco)
– Procedures Established in Main OR and
Ambulatory Surgery
– Cynthia to be notified 30 minutes before
specimen to be ready on cases identified for CTRF eligibility
– In-service given to OR staff to address new
procedure
– Bone Marrow Biopsy patients are being
consented directly after procedure
Specimens Acquired
Organ Breast Bone Marrow Ovary Brain Number of Specimens 8 14 3 0
Manual Form for Tissue Acquisition
Histopathologic Parameters
Tissue Acquisition Database
• Access Database • To Contain Inova and VCU Cases • Demo Today after Leadership Meeting
Tissue Utilization(1)
Non-anonymized tissue samples are a form of patient medical record The health system where the medical record is created is responsible for access and integrity.
Personal identifying information should be maintained behind a health systems firewall.
Tissue Utilization(2)
Each health system which creates non-anonymized human tissue sample banks will:
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identify a guardian who is responsible for maintenance of the integrity of the collection and monitoring utilization.
establish a tissue utilization committee to formulate criteria for use of samples.
Institutional Tissue Utilization Committee
Formulate criteria for who is eligible to obtain human residual samples at the institution.
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Faculty status, IRB approval, ?scientific validity
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?minimum QA requirements ?minimum data access requirements Review requests for human tissue utilization.
Formulate criteria for the degree of clinical information which can be provided with the samples.
Assess resources required to fill request and whether PI is prepared to provide them.
Tissue Utilization(3)
For purposes of regulating utilization of all samples collected by CTRF tissue collection personnel for the CTRF Ca Genomics Project, it is assumed that:
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the VCU and Inova tissue utilization committees agree to follow the criteria and decisions regarding tissue utilization as determined by the CTRF Ca Genomics Project Tissue Utilization Group.
CTRF Ca Genomics Project Tissue Utilization Group
• • • •
Project PIs Tissue Guardians ?Other Project Leadership Issues
– – – – QA Program Pre-Analytical Tissue Handling • Storage Conditions (Freezer Monitoring, etc) Manner in which tissue is supplied Storage and availability of data
Tissue Utilization Summary
VCU Tissue Committee Inova Tissue Committee
CTRF Tissue Utilization Group Analyze Samples
Database Design/Clinical Info
Clinical Data Elements
Define minimal set of common clinical data elements; Initial choice to be the elements required to be sent to state cancer registry Data elements should include MIAME (Minimum Information about a Microarray Experiment) for holding Expression Array Data GeneX Database – Initial choice for storing project data
Database Design/Data Analysis
GeneX Database (Update)
GMU
VCU
“Terabyte” Database – (Update)
VCU
LabBook (Update - Buck)
VCU
QA/QC
Schema (VCU Preliminary)
16 Chips Test for Variation Chip-Chip Labeling Buffers Modules (4)
Update – VCU/GMU
Normalization and Controls
Method Description Arabidopsis The MWG 10K human oligo set comes with arabidopsis controls for hybridization verification. Positive controls for hybridization. Housekeeping Genes spotted to determine the basal level of expression Pin Normalization To normalize the variation in deposition of oligos by the spotting pins Spiking 3’/5’ Ratio Global Dynamic Range Yellow slide Two slides/ Flip Known amounts of labeled oligo, which are specific for a subset of arrayed probes, are included in the hybridization fluid.
The 3’ and 5’ end of certain defined genes will be arrayed. The ratio of the intensities will be taken as an indication of the mRNA degradation The global intensity average will be used to normalize the intensity of the individual spots.
A subset of oligos are spotted in a concentration gradient, and the hybridization buffer is spiked with the labeled complement. The resulting intensity gradient yields information on hybridization uniformity, sensitivity, and dynamic range. The dynamic range yields info on validity of signal as a function of the signal to noise ratio.
An mRNA sample is labeled with both Cy3 and Cy5 in equal ratios. After hybridization the slide is used to balance the laser power. Each microarray experiment will be done on 4 slides. mRNA (Sample and Control) is each labeled with two dyes. 2 slides are hybridized with RED Sample and GREEN Control, 2 slides are hybridized with GREEN Sample and RED Control.
Suggestions for Array Design Among CTRF Members • Spiking: Include the same spiking genes used on the Affy chip, on the C3B and GMU chips • 3’/5’ controls: Include the same genes used on the Affy chip. Can they be added to the GMU chip?
•Dynamic Range: This can be implemented on the C3B and GMU chips.
• Pin Normalization: This is a statistical routine in the R software package, this can be implemented on the C3B and GMU chip. • 5 Slide Experimental Design
5 Slide Experimental Design
1 2 3
1-Yellow 2-Std 3-Flip
C C 1 C S 2 S C 3 2/1=Actual Fold change Std = 2’ 3/1=Actual Fold change Flip = 3’ 2’/3’=1
Microarray Format for the MWG 10K Human Oligo Set
Replicate Array 1
KEY
Houskeeping Spiking & 3’/5’ Dynamic Range Empty Replicate Array 2 16.55 mm 66.95 mm
Establish Standing Weekly or Biweekly Meeting Dates and Times
Complete the Milestone Updates
Document Discussions and Progress Using Listservs
Communication Amongst Members and Focus Groups CG-TISBK: Tissue Bank CG-CLNDT: Clinical and Pathology Data CG-DBDSN: Database Design CG-ANLDT: Analyze Data (Data Analysis) CG-QAQC: QAQC CG-LDRPI: Focus Group Leaders and PIs CG-MEMBS: All Members
LISTSERVS
Address messages to: listname @VENUS.VCU.EDU
Unsubscribe to the listserv by submitting a message with the words
SIGNOFF
listname
Subscribe (C.Garrett) to the listserv by asking the PI with whom you work to submit your name and E-mail address to the Program Director USE the listserv(s) your activity or to seek advice from the members.
to inform members of
Old Business
New Business
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C3B Presentations at BECON2002 Symposium
CTRF - Specific Reportables - - Reminder - -
Intellectual property reporting - licenses, patents, etc Publications
New applications
CTRF Administrative office
will search for new funding opportunities (SPIN)
will collect CVs, other support, facilities, interest documents
goal - 4 - 8 million in d.c. from CTRF CG Project
5/21/02 - 1 million (1yr) submission to VTSF (Penberthy-PI)
Any other discoveries Federal money leveraged Private research money leveraged Advancement of technology and economic development in VA